Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/QEQ/fix_qeq_shielded.cpp
775e8f3cc8f5lammm-master-deprecated

Last Change
Raw File

fix_qeq_shielded.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "fix_qeq_shielded.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "kspace.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixQEqShielded::FixQEqShielded(LAMMPS *lmp, int narg, char **arg) :
FixQEq(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
void FixQEqShielded::init()
{
if (!atom->q_flag)
error->all(FLERR,"Fix qeq/shielded requires atom attribute q");
ngroup = group->count(igroup);
if (ngroup == 0) error->all(FLERR,"Fix qeq/shielded group has no atoms");
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
int ntypes = atom->ntypes;
memory->create(shld,ntypes+1,ntypes+1,"qeq:shielding");
init_shielding();
int i;
for (i = 1; i <= ntypes; i++) {
if (gamma[i] == 0.0)
error->all(FLERR,"Invalid param file for fix qeq/shielded");
}
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixQEqShielded::init_shielding()
{
int i,j;
double d7, swa2, swa3, swb2, swb3;
int ntypes = atom->ntypes;
for( i = 1; i <= ntypes; ++i )
for( j = 1; j <= ntypes; ++j )
shld[i][j] = pow( gamma[i] * gamma[j], -1.5 );
if (fabs(swa) > 0.01 && comm->me == 0)
error->warning(FLERR,"Fix qeq has non-zero lower Taper radius cutoff");
if (swb < 0)
error->all(FLERR, "Fix qeq has negative upper Taper radius cutoff");
else if (swb < 5 && comm->me == 0)
error->warning(FLERR,"Fix qeq has very low Taper radius cutoff");
d7 = pow( swb - swa, 7 );
swa2 = swa*swa;
swa3 = swa2*swa;
swb2 = swb*swb;
swb3 = swb2*swb;
Tap[7] = 20.0 / d7;
Tap[6] = -70.0 * (swa + swb) / d7;
Tap[5] = 84.0 * (swa2 + 3.0*swa*swb + swb2) / d7;
Tap[4] = -35.0 * (swa3 + 9.0*swa2*swb + 9.0*swa*swb2 + swb3 ) / d7;
Tap[3] = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3 ) / d7;
Tap[2] =-210.0 * (swa3*swb2 + swa2*swb3) / d7;
Tap[1] = 140.0 * swa3 * swb3 / d7;
Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 +
7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7;
}
/* ---------------------------------------------------------------------- */
void FixQEqShielded::pre_force(int vflag)
{
if (update->ntimestep % nevery) return;
nlocal = atom->nlocal;
if( atom->nmax > nmax ) reallocate_storage();
if( nlocal > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE )
reallocate_matrix();
init_matvec();
matvecs = CG(b_s, s); // CG on s - parallel
matvecs += CG(b_t, t); // CG on t - parallel
calculate_Q();
if (force->kspace) force->kspace->qsum_qsq();
}
/* ---------------------------------------------------------------------- */
void FixQEqShielded::init_matvec()
{
compute_H();
int inum, ii, i;
int *ilist;
inum = list->inum;
ilist = list->ilist;
for( ii = 0; ii < inum; ++ii ) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
Hdia_inv[i] = 1. / eta[ atom->type[i] ];
b_s[i] = -( chi[atom->type[i]] + chizj[i] );
b_t[i] = -1.0;
t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] );
s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]);
}
}
pack_flag = 2;
comm->forward_comm_fix(this); //Dist_vector( s );
pack_flag = 3;
comm->forward_comm_fix(this); //Dist_vector( t );
}
/* ---------------------------------------------------------------------- */
void FixQEqShielded::compute_H()
{
int inum, jnum, *ilist, *jlist, *numneigh, **firstneigh;
int i, j, ii, jj;
double **x;
double dx, dy, dz, r_sqr, r;
int *type = atom->type;
x = atom->x;
int *mask = atom->mask;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// fill in the H matrix
m_fill = 0;
r_sqr = 0;
for( ii = 0; ii < inum; ii++ ) {
i = ilist[ii];
if (mask[i] & groupbit) {
jlist = firstneigh[i];
jnum = numneigh[i];
H.firstnbr[i] = m_fill;
for( jj = 0; jj < jnum; jj++ ) {
j = jlist[jj];
j &= NEIGHMASK;
dx = x[j][0] - x[i][0];
dy = x[j][1] - x[i][1];
dz = x[j][2] - x[i][2];
r_sqr = dx*dx + dy*dy + dz*dz;
if (r_sqr <= cutoff_sq) {
H.jlist[m_fill] = j;
r = sqrt(r_sqr);
H.val[m_fill] = 0.5 * calculate_H( r, shld[type[i]][type[j]] );
m_fill++;
}
}
H.numnbrs[i] = m_fill - H.firstnbr[i];
}
}
if (m_fill >= H.m) {
char str[128];
sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n",
m_fill, H.m );
error->warning(FLERR,str);
error->all(FLERR,"Fix qeq/shielded has insufficient QEq matrix size");
}
}
/* ---------------------------------------------------------------------- */
double FixQEqShielded::calculate_H( double r, double gamma )
{
double Taper, denom;
Taper = Tap[7] * r + Tap[6];
Taper = Taper * r + Tap[5];
Taper = Taper * r + Tap[4];
Taper = Taper * r + Tap[3];
Taper = Taper * r + Tap[2];
Taper = Taper * r + Tap[1];
Taper = Taper * r + Tap[0];
denom = r * r * r + gamma;
denom = pow(denom,0.3333333333333);
return Taper * EV_TO_KCAL_PER_MOL / denom;
}
c4science · Help